How to complete Order/Chaos in Marathon

After smashing glass to appease MIDA in Marathon, the rebellious Gantry will give you the Order/Chaos priority contract. Staying on theme with the faction, you're sticking it to the UESC, this time by triggering alarms and hacking into encrypted data across Dire Marsh.

Surprise, surprise, that's easier said than done. You've got three different objectives to complete in a single run, sending you from one side of Dire Marsh to the other, and it's not exactly clear what you're looking for.